AMBER Archive (2008)

Subject: Re: AMBER: Combine mdcrd

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jan 04 2008 - 10:44:55 CST

once you produce the stripped traj file you will need a prmtop to match
it. it isn't clear what you mean by "weird structures". are you using the
prmtop with water and pop to view the traj that does not have them?

On Jan 4, 2008 11:37 AM, Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> I am getting weird structures by combining mdcrd with either one
> combine_mdcrd.ptraj:
>
>
> trajin prod1.mdcrd.gz
> trajin prod2.mdcrd.gz
> trajin prod3.mdcrd.gz
> trajout prod1-3_no_wat_pop.mdcrd
> strip :WAT
> strip :POP
>
>
> trajin prod1.mdcrd.gz
> trajin prod2.mdcrd.gz
> trajin prod3.mdcrd.gz
> trajout prod1-3_no_wat.mdcrd
> strip :WAT
>
> Then:
>
> ptraj my.prmtop < combine_mdcrd.ptraj
>
> where my.prmtop is the one for the original trajectories to combine.
>
> It deals of a protein complex in a POPC membrane, all in a water box. Even
> the
> structure of the non-polymeric ligand is completely disordered. Of course,
> each
> trajectory to combine is OK. If anything, prod1 was obtained with 0.002fstime
> step, the other two with 0.0015fs timestep.
>
> Should prmtop be regenerated (how?) to get all fitting? My final aim is to
> carry out a cluster analysis.
>
> Additionally, once the above is set in order, it is not clear to me how to
> add
> to the ptraj script the request for rmsd for both the protein and the
> ligand.
>
> Thanks
> francesco pietra
>
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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